Wataru IWASAKI, Ph.D.
iwasaki AT k.u-tokyo.ac.jp
- Professor, the University of Tokyo
- - Department of Integrated Biosciences, Graduate School of Frontier Sciences
- - Department of Biological Sciences, Graduate School of Science (adjunct)
- - Department of Bioinformatics and Systems Biology, Faculty of Science (adjunct)
- - Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences (adjunct)
- - Atmosphere and Ocean Research Institute (adjunct)
- - Institute for Quantitative Biosciences (adjunct)
- - Collaborative Research Institute for Innovative Microbiology (adjunct)
Iwasaki Lab
Dept Integrated Biosci, UTokyo
Mission and Research Topics
The field of biology has expanded from the traditional approaches of focusing on specific organisms and phenomena to utilizing data science approaches in the pursuit of obtaining a comprehensive understanding of life. Under this context, our laboratory employs interdisciplinary approaches, including but not limited to: bioinformatics, laboratory experiments, mathematics, and field samplings to study evolution and ecology of diverse life forms, and to develop novel biotechnological methods.
Research Keywords and Topics:
- Evolutionary and ecological bioinformatics
- Evolution of genomes and life systems
- Microbial dark matter, non-model organisms
- Microbial ecology, metagenomics
- Environmental DNA
In particular, we are aiming at the following fundamental research questions:
(1) How have the elaborate and complex living systems evolved?
(2) How are the ecosystems stably maintained?
(3) What unknown gene functions have evolved in 4 billion years?
(4) What is the methodology to reveal unknown gene functions from big data?
(5) How many genes are being born on the earth?
Publications
Please refer to our Full Publication List.
Selected Papers
- Konno and Iwasaki. Science Advances (2023)
- Zhu, [...], Iwasaki. Molecular Biology and Evolution (2023)
- Plianchaisuk, [...], and Iwasaki. Molecular Biology and Evolution (2022)
- Fukunaga and Iwasaki. Bioinformatics Advances (2022)
- Mikami and Iwasaki. Methods in Ecology and Evolution (2021)
- Mise and Iwasaki. iScience (2020)
- Matsui and Iwasaki. Systematic Biology (2020)
- Hiraoka, [...], and Iwasaki. Nature Communications (2019)
- Needham, Yoshizawa, Hosaka, [...], Iwasaki*, and Worden*. PNAS (2019)
- Cosentino and Iwasaki. Bioinformatics (2019)
- Kumagai, [...], and Iwasaki. The ISME Journal (2018)
- Sato, [...], and Iwasaki. Molecular Biology and Evolution (2018)
- Sriswasdi, Yang, and Iwasaki. Nature Communications (2017)
- Sriswasdi, [...], and Iwasaki. Genome Research (2016)
- Miya, [...], and Iwasaki. Royal Society Open Science (2015)
- Aoki, Ito, and Iwasaki. Molecular Biology and Evolution (2013)
- Iwasaki et al. Molecular Biology and Evolution (2013)
- Praneenararat, Takagi, and Iwasaki. Bioinformatics (2011)
- Iwasaki and Takagi. PLOS Genetics (2009)
- Iwasaki and Takagi. Bioinformatics (2007)
- Iwasaki et al. Journal of Molecular Biology (2006)
Joining Iwasaki Lab at UTokyo
As a Graduate Student
We are accepting graduate students as faculty of the following departments at the University of Tokyo. Whereas they have different systems of lectures, degrees, and scholarships, students of both departments spend laboratory life similarly.
We highly welcome those who majored in bioinformatics and/or were involved in research projects related to bioinformatics during their undergraduate or master courses, and aim at earning a Ph.D by pursuing the research goals described above. If you are interested in joining our lab, please examine our publication list and email iwasaki AT k.u-tokyo.ac.jp.
Department of Integrated Biosciences (Graduate School of Frontier Sciences, UTokyo)
- Graduate School of Frontier Sciences also provides instructions for international students, financial support, admission option with scholarship programs, as well as Summer Internship Program (UTSIP Kashiwa) for undergraduate students. Note that Iwasaki Lab is named as Laboratory of Computational Evolutionary Biology in Department of Integrated Biosciences.
Department of Biological Sciences (Graduate School of Science, UTokyo)
- Graduate School of Science provides admission, scholarship, and other information for international students.
Notes: We have experience in accepting students from outside of Japan. Japanese language is not mandatory if you have enough English skills; however, a will to learn Japanese would be necessary because it makes you enjoy Japan more, and many optional classes are held in Japanese. As the University of Tokyo provides Japanese language classes, we usually encourage colleagues from abroad to take them. Also, we highly encourage international students to obtain scholarships because of financial support and credit for life in Japan (Also refer to the information provided by UTokyo International Education Support Office and Japan Student Services Organization). The best one would be Japanese Government Scholarship (Ministry of Education, Culture, Sports, Science and Technology (Monbukagakusho or MEXT) Scholarship). Please consult with your local Japan Embassy for the selection information. In addition, International Student Handbook and Information for Prospective Students are available at UTokyo website.
As a Postdoctoral Fellow
If you are interested in pursuing the research goals described above in our laboratory, please examine our publication list and email iwasaki AT k.u-tokyo.ac.jp. Information on our post-doc position availability may be posted in JREC-IN Portal, or we might have an open position even if there is no posted information. In addition, we may help you obtain fellowships such as Postdoctoral Fellowships for Research in Japan (Japan Society for the Promotion of Science) and Human Frontier Science Program Postdoctoral Fellowships.
Notes: We have experience in accepting Postdoctoral Fellows from outside of Japan. Japanese language is not mandatory if you have enough English skills; however, to enjoy life in Japan, a will to learn Japanese to some extent would be necessary. As the University of Tokyo provides Japanese language classes, we usually encourage colleagues from abroad to take them. For more information about life on the Kashiwa Campus, please also refer to the website of International Liaison Office at the Graduate School of Frontier Sciences, UTokyo.
Profile of Wataru IWASAKI (in 2023Apr)
2021Apr
Professor at the University of Tokyo
- Department of Integrated Biosciences, Graduate School of Frontier Sciences
- Department of Biological Sciences, Graduate School of Science (adjunct)
- Department of Bioinformatics and Systems Biology, Faculty of Science (adjunct)
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences (adjunct)
- Atmosphere and Ocean Research Institute (adjunct)
- Institute for Quantitative Biosciences (adjunct)
- Collaborative Research Institute for Innovative Microbiology (adjunct)
2014Apr
Associate Professor at the University of Tokyo
- Department of Biological Sciences, Graduate School of Science
2011Jul
Assistant Professor at the University of Tokyo
- Center for Earth Surface System Dynamics, Atmosphere and Ocean Research Institute
2009Apr
Research Associate at the University of Tokyo
- Department of Computational Biology, Graduate School of Frontier Sciences
2009Mar Ph.D., Department of Computational Biology, the University of Tokyo
2007Mar Master of Science, Department of Computational Biology, the University of Tokyo
2005Mar Completed, Undergraduate Program for Bioinformatics and Systems Biology, the University of Tokyo
2005Mar Bachelor of Science, Department of Biophysics and Biochemistry, the University of Tokyo
1983 Mar Born in Fuchu, Tokyo.
Awards
Mid-career Researcher Award, Society of Genome Microbiology, Japan (2021)
Mid-career Researcher Award, Japanese Society of Microbial Ecology (2019)
The Commendation for Science and Technology by the Minister of Education, Culture, Sports, Science and Technology of Japan (The Young Scientists' Prize) (2019)
Oxford Journals - Japanese Society for Bioinformatics Prize, Japanese Society for Bioinformatics (2018)
Young Scientist Initiative Award, The Society of Evolutionary Studies, Japan (2018)
Dean Prize, Graduate School of Frontier Sciences, the University of Tokyo, as the Conference Chair of The 2nd Taiwan-Japan Young Researchers Conference on Computational and Systems Biology (2009)
Dean Prize, Graduate School of Frontier Sciences, the University of Tokyo (2007)
Other Affiliations
Science Council of Japan and Young Academy of Japan
SCJ Website
YAJ Website
Member
- 2020Oct-2023Sep (25th) (Subcommittee on Bioinformatics, Subcommittee on Evolutionary Studies, Subcommittee on Integrative Microbiology, Subcommittee on Molecular Biology, Young Academy of Japan (President))
- 2017Oct-2020Sep (24th) (Subcommittee on Bioinformatics, Subcommittee on Evolutionary Studies (Secretary), Young Academy of Japan (Secretary), Subcommittee on Young Scientist Network (Chair), Subcommittee on GYA Annual Meeting, Subcommittee on Academic Systems, Committee on Public Information, Subcommittee on Homepage)
- 2016Jan-2017Sep (23rd) (Young Academy of Japan, Subcommittee on Young Scientist Network (Secretary))
Global Young Academy
GYA Website
Member
- 2017May-2022Jun
Alumnus Plus
- 2022Jun-2023Jun
Institute for Chemical Research, Kyoto University
KUICR Website
Visiting Associate Professor
- 2015Apr-2016Mar
Database Center for Life Science, Research Organization of Information and Systems
DBCLS Website
Project Collaborator
- 2010Apr-2018Mar
Academic Societies
International Society for Computational Biology
ISCB Website
Board of Directors
- 2021Jan-2024Jan
- 2018Jan-2021Jan
Nomination Committee Member
- 2021Nov-
EvolCompGen COSI Website
Committee Member of Evolution & Comparative Genomics COSI (Community of Special Interest)
- 2017Nov-
Japanese Society for Bioinformatics
JSBi Website
President
- 2019Apr-2021Mar
Vice President
- 2018Apr-2019Mar
- 2017Apr-2018Mar
Board of Directors (Councilor)
- 2020Apr-2022Mar
- 2018Apr-2020Mar
- 2016Apr-2018Mar
- 2013Apr-2015Mar
- 2011Apr-2013Mar
Manager
- 2022Apr-2023Mar
- 2021Apr-2022Mar
- 2020Apr-2021Mar
- 2019Apr-2020Mar
- 2018Apr-2019Mar
- 2017Apr-2018Mar
- 2016Apr-2017Mar
- 2015Apr-2016Mar
- 2014Apr-2015Mar
Japanese Society of Microbial Ecology
JSME Website
Councilor
- 2023Jan-2025Mar
- 2021Jan-2022Dec
- 2017Jan-2018Dec
- 2015Jan-2016Dec
Career Path and Diversity Committee (reorganized from Gender Equality and Diversity Committee in 2019Sep)
- 2013Dec-
Gender Equality and Diversity Working Group
- 2013Mar-2013Nov
New Award Planning Committee
- 2022Jun-
Mid-career Award Committee
- 2022Apr-2022May
The Molecular Biology Society of Japan
MBSJ Website
Career Path Committee
- 2015Jan-2016Dec
- 2013Jan-2014Dec
Life Science Education Committee
- 2021Jan-2022Dec
The eDNA Society
eDNA Society Website
Board of Directors
- 2020Nov-2022General Meeting
- 2018Sep-2020Nov
- 2018Apr-2018Sep
The Society of Evolutionary Studies, Japan
SESJ Website
Representative
- 2020Jul-2022Jun
- 2018Jul-2020Jun
Society of Genome Microbiology, Japan
SGMJ Website
Councilor
- 2021Jan-2023Dec
Young Researchers Group for Computational/Omics/Systems Biology in Japan
Bioinfowakate Website
President
- 2009Feb-2011Mar
Board Member
- 2009Feb-2015Mar
NGS-Field (Japanese Community for Researches Using NGS)
NGS-Field Website
President
- 2014Feb-2016May
Board Member
- 2010Oct-
Journal Editors and Advisors
Bioinformatics Advances
Bioinformatics Advances Website
Editorial Board
- 2021 Nov-
Microbes and Environments
Microbes and Environments Website
Associate Editor
- 2017Jun-
Scientific Reports
Scientific Reports Website
Editorial Board Member
- 2017Feb-2021Aug
Mendeley
Mendeley Advisor
- 2012Dec-
Conference Committees
Program Committee, The 2023 Annual Conference of the Japanese Society for Bioinformatics (Sep 2023, Kashiwanoha conference center, Kashiwa, Chiba, Japan)
Proceeding Committee and Abstract Co–chair (COSI on Evolution & Comparative Genomics), The 31st Conference on Intelligent Systems for Molecular Biology and the 22nd European Conference on Computational Biology (ISMB/ECCB2023) (Jul 2023, Centre de Congrès de Lyon, Lyon, France)
Program Committee, Research in Computational Molecular Biology – Comparative Genomics in 2023 (RECOMB-CG2023) (Apr 2023, Marriott Sisli, Istanbul, Turkey)
Program Committee, GIW XXXI/ISCB-Asia V (GIW/ISCB Asia 2022) (Dec 2022, National Cheng-Kung University, Tainan, Taiwan)
Proceeding Committee and Abstract Co–chair (COSI on Evolution & Comparative Genomics), The 30th Conference on Intelligent Systems for Molecular Biology (ISMB2022) (July 2022, Hilton Madison Monona Terrace and Madison Concourse and Governor's Club hotels, Madison, USA)
Local Organizing Committee, 2022 Global Young Academy Annual General Meeting and Conference (Jun 2022, Kyushu University, Japan)
Program Committee, Research in Computational Molecular Biology – Comparative Genomics in 2022 (RECOMB-CG2022) (May 2022, University of California, San Diego, La Jolla, USA)
Program Committee, The 42nd Annual Meeting of the Molecular Biology Society of Japan (Dec 2021, Pacifico Yokohama, Yokohama, Japan)
Executive Committee, The 2021 Annual Conference of the Japanese Society for Bioinformatics (Sep 2021, Online)
Program Committee, Research in Computational Molecular Biology – Comparative Genomics in 2021 (RECOMB-CG2021) (Sep 2021, Online)
Proceedings Committee Area Chair (Evolutionary, comparative and population genomics) and COVID-19 Track Committee, The 29th Conference on Intelligent Systems for Molecular Biology and the 20th European Conference on Computational Biology (ISMB/ECCB2021) (Jul 2021, Online)
Conference Committee, The 22nd Annual Meeting of the Society of Evolutionary Studies, Japan (Sep 2020, Online)
Steering Committee, GIW/ISCB-Asia 2020 (Dec 2020, Tainan, Taiwan)
Proceedings Committee Area Chair (Population Genomics and Molecular Evolution), The 28th annual international conference on Intelligent Systems for Molecular Biology (ISMB2020) (Jul 2020, Palais des congrès de Montréal, Montréal, Canada)
Program Committee, Joint 30th International Conference on Genome Informatics and Australian Bioinformatics And Computational Biology Society Annual Conference (GIW/ABACBS2019) (Dec 2019, University of Sydney, Sydney, Australia)
Poster Committee, The 42nd Annual Meeting of the Molecular Biology Society of Japan (Dec 2019, Fukuoka International Congress Center and Marine Messe Fukuoka, Fukuoka, Japan)
Organizer, Quest for Orthologs 6 (Jul-Aug 2019, National Institute for Basic Biology, Okazaki, Japan)
Proceeding Committee, The 27th Conference on Intelligent Systems for Molecular Biology and the 18th European Conference on Computational Biology (ISMB/ECCB 2019) (Jul 2019, Congress Center Basel, Basel, Switzerland)
Executive Committee, The 20th Annual Meeting of the Society of Evolutionary Studies, Japan (Aug 2018, Komaba Campus of the University of Tokyo, Tokyo, Japan)
Proceeding Committee, The 26th Conference on Intelligent Systems for Molecular Biology (ISMB2018) (Jul 2018, Hyatt Regency Hotel, Chicago, USA)
Abstract Co-chair (COSI on Evolution & Comparative Genomics), The 26th Conference on Intelligent Systems for Molecular Biology (ISMB2018). (Jul 2018, Hyatt Regency Hotel, Chicago, USA)
Program Committee, The 16th Asia Pacific Bioinformatics Conference (APBC2018) (Jan 2018, Hiyoshi Campus of Keio University, Yokohama, Japan)
Program Committee, The 28th International Conference on Genome Informatics (GIW2018) (Oct-Nov 2017, Hotel Samjung, Seoul, Korea)
Preparatory Committee, The Joint Meeting of Japanese Environmental Microbiology-related Associations 2017 (Aug 2017, Kawauchi Campus of Tohoku University, Sendai, Japan)
Conference Chair Advisor, The 5th Meeting of Japanese Community for Researches Using NGS (May 2017, Sendai International Center, Sendai, Japan)
Organizing Committee, The 10th Annual Meeting of Society of Genome Microbiology, Japan (Mar 2016, Ookayama Campus of Tokyo Institute of Technology, Tokyo, Japan)
Program Committee, The 4th Joint Conference on Informatics in Biology, Medicine, and Pharmacology. (The 2015 Annual Conference of the Japanese Society for Bioinformatics) (Oct 2015, Uji Campus of Kyoto University, Uji, Japan)
Conference Chair, The 4th Meeting of Japanese Community for Researches Using NGS (Jul 2015, Tsukuba International Congress Center, Tsukuba, Japan)
Program Committee, The 25th International Conference on Genome Informatics (GIW2014) (Dec 2014, Tokyo, Japan)
Organizing Committee, The 37th Annual Meeting of the Molecular Biology Society of Japan (Nov 2014, Pacifico Yokohama, Yokohama, Japan)
Organizing Member, The 5th Meeting of Young Researchers Group for Computational/Omics/Systems Biology in Japan (Feb 2014, Kemigawa Seminar House of the University of Tokyo, Chiba, Japan)
Organizing Committee, The 2nd Joint Conference on Informatics in Biology, Medicine, and Pharmacology (The 2013 Annual Conference of the Japanese Society for Bioinformatics) (Oct 2013, Tower Hall Funabori, Tokyo, Japan)
Organizing Member, The 3rd Meeting of Japanese Community for Researches Using NGS (Sep 2013, Kobe International Conference Center, Kobe, Japan)
Organizing Member, The 4th Meeting of Young Researchers Group for Computational/Omics/Systems Biology in Japan (Mar 2013, National Institute for Basic Biology, Okazaki, Japan)
Organizing Committee, The 1st Joint Conference on Informatics in Biology, Medicine, and Pharmacology (The 2012 Annual Conference of the Japanese Society for Bioinformatics) (Oct 2012, Tower Hall Funabori, Tokyo, Japan)
Program Committee, The 1st Joint Conference on Informatics in Biology, Medicine, and Pharmacology (The 2012 Annual Conference of the Japanese Society for Bioinformatics) (Oct 2012, Tower Hall Funabori, Tokyo, Japan)
Program Committee, Recommender System Challenge (RecSysChallenge 2012), ACM Recommender Systems 2012 (Sep 2012, Dublin, Ireland)
Organizing Member, The 2nd Meeting of Japanese Community for Researches Using NGS (May 2012, Hotel Hankyu Expo Park, Suita, Japan)
Organizing Member, The 3rd Meeting of Young Researchers Group for Computational/Omics/Systems Biology in Japan (Oct 2011, National Institute for Basic Biology, Okazaki, Japan)
Organizing Member, The 1st Meeting of Japanese Community for Researches Using NGS (May 2011, Atami New Fujiya Hotel, Atami, Japan)
Advisory Committee, The 4th Asian Young Researchers Conference on Computational and Omics Biology (4th AYRCOB) (Dec 2010, Biopolis, Singapore)
Organizing Member, The 2nd Meeting of Young Researchers Group for Computational/Omics/Systems Biology in Japan (Oct 2010, National Intitute of Genetics, Mishima, Japan)
Organizing Committee, The 3rd Asian Young Researchers Conference on Computational and Omics Biology (3rd AYRCOB) (Mar 2010, National Cheng Kung University, Tainan, Taiwan)
Organizing Member, The 1st Meeting of Young Researchers Group for Computational/Omics/Systems Biology in Japan (Apr 2009, National Intitute of Genetics, Mishima, Japan)
Conference Chair, The 2nd Taiwan-Japan Young Researchers Conference on Computational and Systems Biology (Nov 2008, Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan)
Organizing Committee, The 1st Japan-Taiwan Young Researchers Conference on Computational and Systems Biology (Mar 2008, National Tsing Hua University, Hsinchu, Taiwan)
Note: The general introduction to AYRCOB can be found here.
Tools and Databases
MitoFish & MitoAnnotator
MitoFish & MitoAnnotator- Fish mitochondrial genome database and annotator.
MiFish Pipeline
MiFish Pipeline- Pipeline for analyzing fish environmental DNA data.
SonicParanoid
SonicParanoid- SonicParanoid is a fast, accurate, and easy-to-use software tool for the identification of orthologous relationships among multiple genomes.
Evodictor
Evodictor- Evodictor is software for predicting genome evolution by gene gains and losses.
Graph Splitting
Graph Splitting- Graph Splitting is a phylogenetic tree reconstruction method for resolving early evolution of protein families without multiple sequence alignment.
ProkAtlas
ProkAtlas- ProkAtlas is a database and analysis pipeline that infer habitat environment of prokaryotes from 16S rRNA gene sequences.
Fern Tree of Life
Fern Tree of Life- Fern Tree of Life is an updated and comprehensive phylogenetic tree of ferns.
Logicome Profiler
Logicome Profiler- Logicome Profiler is a method to exhaustively detect statistically significant triplet logic relationships from a binary matrix dataset (e.g., ortholog table).
Mirage
Mirage- Mirage (MIxtuRe model for Ancestral Genome Estimation） reconstructs gene copy-number evolution by allowing different gene families to have flexible gene gain/loss rates.
Inverse Potts Model for phylogenetic profiling
Inverse Potts Model- Inverse Potts Model reduces spurious correlation bias in phylogenetic profiling, a powerful computational method for revealing the functions of function-unknown genes.
Flipping t-ratio Test
Flipping t-ratio Test- Flipping t-ratio test accurately tests the Pareto theory by considering phylogenetic background as well as artifacts that can be induced during dimensionality reduction.
MetaMetaDB
MetaMetaDB- MetaMetaDB is a 16S rRNA database for revealing which environments the species bearing the query 16S rRNA(s) can be found.
GroupTracker
GroupTracker- GroupTracker is a multiple animal tracking system that tracks individuals under severe occlusion.
MOCCS (Motif Centrality Analysis of ChIP-Seq)
MOCCS for ChIP-Seq Analysis- A bioinformatic method that enumerates and evaluates all significant DNA-binding motifs based on ChIP-Seq datasets.
Image Manipulation Detector
Image Manipulation Detector- Software for automatically detecting manipulated images in life science.
TogoDoc Client
TogoDoc Client- Efficient management and smart recommendation of life science literature, for Windows and MacOSX.
TogoDoc Mobile
TogoDocMobile@AppStore- iPhoneApp of TogoDoc.
Wheel Tree
Wheel Tree- Wheel Tree is an Intuitive, Informative, and Most Balanced representation of phylogenetic trees.
Arabimarklet: Useful Bookmarklets for Plant Researchers
NaviCluster
NaviCluster- Interactive navigation of large and complicated biological networks, in a Google-Maps like manner.
NaviClusterCS
NaviClusterCS for CytoScape- CytoScape plug-in version of NaviClusger.
Quest for Otrhologs
Quest for Orthologs Website- Quest for Orthologs is an international bioinformatics community for analyzing evolutionary relationships among genes, especially for developing computational methods for estimating orthologs.
